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fix enums for data service

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This commit is contained in:
Nicola Tarocco 2023-12-12 19:04:21 +01:00 committed by Luis Aleixo
parent d79ef934cb
commit 00ff1af71d
4 changed files with 57 additions and 29 deletions
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13
caimira/apps/calculator/__main__.py
View file

@ -35,12 +35,23 @@ def configure_parser(parser) -> argparse.ArgumentParser:
return parser
def _init_logging(debug=False):
# Set the logging level for urllib3 and requests to WARNING
logging.getLogger("urllib3").setLevel(logging.WARNING)
logging.getLogger("requests").setLevel(logging.WARNING)
# set app root log level
logger = logging.getLogger()
root_log_level = logging.DEBUG if debug else logging.WARNING
logger.setLevel(root_log_level)
def main():
parser = configure_parser(argparse.ArgumentParser())
args = parser.parse_args()
debug = args.no_debug
logging.getLogger().setLevel(logging.DEBUG if debug else logging.WARNING)
_init_logging(debug)
theme_dir = args.theme
if theme_dir is not None:

5
caimira/apps/calculator/report_generator.py
View file

@ -220,7 +220,7 @@ def manufacture_conditional_probability_data(
infection_probability: models._VectorisedFloat
):
data_registry: DataRegistry = exposure_model.data_registry
min_vl = data_registry.conditional_prob_inf_given_viral_load['min_vl']
max_vl = data_registry.conditional_prob_inf_given_viral_load['max_vl']
step = (max_vl - min_vl)/100
@ -502,11 +502,12 @@ class ReportGenerator:
now = datetime.utcnow().astimezone()
time = now.strftime("%Y-%m-%d %H:%M:%S UTC")
data_registry_version = f"v{model.data_registry.version}" if model.data_registry.version else None
context = {
'model': model,
'form': form,
'creation_date': time,
'data_registry_version': model.data_registry.version,
'data_registry_version': data_registry_version,
}
scenario_sample_times = interesting_times(model)

26
caimira/monte_carlo/data.py
View file

@ -15,24 +15,40 @@ from caimira.store.data_registry import DataRegistry
def evaluate_vl(value, data_registry: DataRegistry):
if value == ViralLoads.COVID_OVERALL:
# FIXME: temp fix until data service values is updated
# remove old Ref value
if "covid_overal_vl_data" in value:
value = ViralLoads.COVID_OVERALL.value
elif "symptomatic_vl_frequencies" in value:
value = ViralLoads.SYMPTOMATIC_FREQUENCIES.value
if value == ViralLoads.COVID_OVERALL.value:
return covid_overal_vl_data(data_registry)
elif value == ViralLoads.COVID_OVERALL:
elif value == ViralLoads.SYMPTOMATIC_FREQUENCIES.value:
return symptomatic_vl_frequencies
else:
raise ValueError(f"Invalid ViralLoads value {value}")
def evaluate_infectd(value, data_registry: DataRegistry):
if value == InfectiousDoses.DISTRIBUTION:
# FIXME: temp fix until data service values is updated
# remove old Ref value
if "infectious_dose_distribution" in value:
value = InfectiousDoses.DISTRIBUTION.value
if value == InfectiousDoses.DISTRIBUTION.value:
return infectious_dose_distribution(data_registry)
else:
raise ValueError(f"Invalid InfectiousDoses value {value}")
def evaluate_vtrr(value, data_registry: DataRegistry):
"""."""
if value == ViableToRNARatios.DISTRIBUTION:
# FIXME: temp fix until data service values is updated
# remove old Ref value
if "viable_to_RNA_ratio_distribution" in value:
value = ViableToRNARatios.DISTRIBUTION.value
if value == ViableToRNARatios.DISTRIBUTION.value:
return viable_to_RNA_ratio_distribution(data_registry)
else:
raise ValueError(f"Invalid ViableToRNARatios value {value}")

42
caimira/store/data_registry.py
View file

@ -210,51 +210,51 @@ class DataRegistry:
}
virus_distributions = {
"SARS_CoV_2": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 1,
"infectiousness_days": 14,
},
"SARS_CoV_2_ALPHA": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 0.78,
"infectiousness_days": 14,
},
"SARS_CoV_2_BETA": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 0.8,
"infectiousness_days": 14,
},
"SARS_CoV_2_GAMMA": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 0.72,
"infectiousness_days": 14,
},
"SARS_CoV_2_DELTA": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 0.51,
"infectiousness_days": 14,
},
"SARS_CoV_2_OMICRON": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 0.2,
"infectiousness_days": 14,
},
"SARS_CoV_2_Other": {
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
"transmissibility_factor": 0.1,
"infectiousness_days": 14,
},